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Crystal structure of phospholipase A1

Analyse Crystal structure of phospholipase A1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YIJ
Type: protein
Length: 776 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase A1-iigamma
EC: 3.1.1.-
UniProt: O49523
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase A1-iigamma (EC 3.1.1.-)	protein	390	31% helix, 18% strand	O49523
B	Phospholipase A1-iigamma (EC 3.1.1.-)	protein	386	32% helix, 19% strand	O49523

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.77	0.79	110	empty
2	204	0.66	0.84	31	empty
3	264	0.62	0.80	36	empty
4	105	0.44	0.78	27	empty
5	85	0.37	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 1489 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

2YIJ · Crystal Structure of phospholipase A1 · the same entry in another collection · chain A against A, TM-score 1.00
O49523 · AlphaFold monomer V2.0 prediction for phospholipase A1-iigamma (O49523) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O49523
Elsewhere: RCSB PDB 2YIJ · PDBe 2YIJ · UniProt O49523

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